# 14 Limitations and Best Practices

## Quick Answer
EVd3x is optimized for fast exploratory analysis with transparent caps and provenance. Robust conclusions require reviewing full exports, not just first-render views.

## What this does
Documents operational caveats and recommended usage patterns.

## Inputs
- Query size and complexity
- User-selected caps and filters

## Outputs
- More stable interpretation workflow
- Clear method reporting for manuscripts

## How calculated
Not a scoring module. This section formalizes interpretation safeguards: inspect truncation flags, report selected parameters, compare filtered vs full exports, and verify source coverage before claims.

## What to download
Always include export manifest and warning files with result tables and figures.

## Known limits
UI responsiveness controls can hide tail distributions in interactive tables. Scientific completeness depends on full-data review.

## Interpretation boundaries

- EV evidence rows mean a molecule was reported in an EV cargo source or linked publication; they do not prove abundance, vesicle subtype, cell of origin, uptake, or function.
- Disease priority ranks curation support, not diagnostic probability or patient-level risk.
- Pathway enrichment is annotation over-representation and is sensitive to background, query size, source granularity, and overlap rules.
- Cell specificity ranks candidate contexts from marker/expression support; it does not infer EV source cell or disease cell state.
- Communication and L-R scores prioritize candidate pairs; they do not prove EV-mediated transfer or receptor activation.
- miRNA-target and bridge scores rank candidate regulatory links; they do not validate repression in the system.
- STRING/PPI edges are high-confidence protein interaction context, not EV-specific interactions.
- Assistant summaries are retrieval-grounded navigation aids and must be checked against tables/exports.

## Reporting checklist

- Report the original query, active mode, top-N, direction, selected node/cell pair, and thresholds.
- Include processing caps when relevant: molecule cap, target-scan cap, cell-specificity scan cap, STRING row cap, and visible-row limits.
- Export the full table for any claim made from a filtered UI panel.
- Preserve source database, PubMed, EV-TRACK, disease source, pathway source, and LR/PPI source fields in downstream figures.